FMO DATABASE

FMODB ID: NNYYQ

Calculation Name: 1NVP-D-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NVP

Chain ID: D

ChEMBL ID:

UniProt ID: P52657

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	97
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-643077.606805
FMO2-HF: Nuclear repulsion	603951.324637
FMO2-HF: Total energy	-39126.282169
FMO2-MP2: Total energy	-39241.654493

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(D:3:TYR)

Summations of interaction energy for fragment #1(D:3:TYR)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-17.152	-6.642	6.384	-6.299	-10.596	-0.005

Interaction energy analysis for fragmet #1(D:3:TYR)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.013

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	D	5	LEU	0	-0.003	-0.029	2.040	-3.793	0.386	3.166	-3.314	-4.031	0.007
4	D	6	TYR	0	-0.005	-0.014	3.280	-0.173	0.528	0.034	-0.069	-0.666	0.000
5	D	7	ARG	1	0.854	0.915	6.636	-0.977	-0.977	0.000	0.000	0.000	0.000
6	D	8	ASN	0	-0.016	0.010	8.870	0.104	0.104	0.000	0.000	0.000	0.000
7	D	9	THR	0	-0.014	-0.017	9.575	-0.032	-0.032	0.000	0.000	0.000	0.000
8	D	10	THR	0	0.074	0.030	12.281	0.030	0.030	0.000	0.000	0.000	0.000
9	D	11	LEU	0	-0.014	-0.003	11.835	0.026	0.026	0.000	0.000	0.000	0.000
10	D	12	GLY	0	0.008	0.008	11.367	0.045	0.045	0.000	0.000	0.000	0.000
11	D	13	ASN	0	0.024	0.006	12.301	0.021	0.021	0.000	0.000	0.000	0.000
12	D	14	SER	0	0.038	0.024	15.003	0.034	0.034	0.000	0.000	0.000	0.000
13	D	15	LEU	0	-0.035	0.002	12.213	0.031	0.031	0.000	0.000	0.000	0.000
14	D	16	GLN	0	-0.027	-0.042	12.327	-0.007	-0.007	0.000	0.000	0.000	0.000
15	D	17	GLU	-1	-0.862	-0.919	15.952	0.049	0.049	0.000	0.000	0.000	0.000
16	D	18	SER	0	0.005	-0.014	19.229	0.002	0.002	0.000	0.000	0.000	0.000
17	D	19	LEU	0	-0.083	-0.049	14.982	0.019	0.019	0.000	0.000	0.000	0.000
18	D	20	ASP	-1	-0.874	-0.953	18.796	0.219	0.219	0.000	0.000	0.000	0.000
19	D	21	GLU	-1	-0.944	-0.952	20.964	0.095	0.095	0.000	0.000	0.000	0.000
20	D	22	LEU	0	-0.010	0.002	21.438	0.002	0.002	0.000	0.000	0.000	0.000
21	D	23	ILE	0	-0.053	-0.019	19.108	0.013	0.013	0.000	0.000	0.000	0.000
22	D	24	GLN	0	-0.056	-0.022	23.591	-0.005	-0.005	0.000	0.000	0.000	0.000
23	D	25	SER	0	-0.080	-0.043	26.285	-0.002	-0.002	0.000	0.000	0.000	0.000
24	D	26	GLN	0	-0.034	-0.036	27.055	-0.007	-0.007	0.000	0.000	0.000	0.000
25	D	27	GLN	0	-0.008	0.004	26.238	0.001	0.001	0.000	0.000	0.000	0.000
26	D	28	ILE	0	-0.047	-0.006	19.841	0.016	0.016	0.000	0.000	0.000	0.000
27	D	29	THR	0	0.020	0.009	21.903	0.006	0.006	0.000	0.000	0.000	0.000
28	D	30	PRO	0	0.097	0.026	19.361	0.026	0.026	0.000	0.000	0.000	0.000
29	D	31	GLN	0	0.000	0.004	16.954	0.113	0.113	0.000	0.000	0.000	0.000
30	D	32	LEU	0	0.035	0.019	16.705	0.086	0.086	0.000	0.000	0.000	0.000
31	D	33	ALA	0	0.089	0.043	16.502	0.040	0.040	0.000	0.000	0.000	0.000
32	D	34	LEU	0	-0.019	-0.015	11.163	0.048	0.048	0.000	0.000	0.000	0.000
33	D	35	GLN	0	-0.011	-0.023	12.007	0.248	0.248	0.000	0.000	0.000	0.000
34	D	36	VAL	0	0.007	0.017	12.471	0.079	0.079	0.000	0.000	0.000	0.000
35	D	37	LEU	0	0.006	0.002	10.110	0.007	0.007	0.000	0.000	0.000	0.000
36	D	38	LEU	0	-0.023	-0.006	7.790	0.163	0.163	0.000	0.000	0.000	0.000
37	D	39	GLN	0	-0.037	-0.013	7.637	0.283	0.283	0.000	0.000	0.000	0.000
38	D	40	PHE	0	0.017	-0.002	8.366	-0.126	-0.126	0.000	0.000	0.000	0.000
39	D	41	ASP	-1	-0.725	-0.833	3.674	1.100	1.318	0.001	-0.042	-0.178	0.000
40	D	42	LYS	1	0.934	0.978	5.128	-2.386	-2.308	-0.001	-0.004	-0.073	0.000
41	D	43	ALA	0	0.009	0.007	6.388	-0.314	-0.314	0.000	0.000	0.000	0.000
42	D	44	ILE	0	-0.008	-0.001	6.106	-0.092	-0.092	0.000	0.000	0.000	0.000
43	D	45	ASN	0	-0.043	-0.051	2.665	-2.533	-0.436	0.222	-0.987	-1.333	-0.008
44	D	46	ALA	0	0.000	0.005	6.318	0.091	0.091	0.000	0.000	0.000	0.000
45	D	47	ALA	0	-0.020	-0.016	9.213	0.019	0.019	0.000	0.000	0.000	0.000
46	D	48	LEU	0	-0.040	-0.021	7.021	0.047	0.047	0.000	0.000	0.000	0.000
47	D	49	ALA	0	0.014	0.020	8.345	0.032	0.032	0.000	0.000	0.000	0.000
48	D	50	GLN	0	-0.008	0.005	10.305	0.018	0.018	0.000	0.000	0.000	0.000
49	D	51	ARG	1	0.938	0.978	13.385	0.142	0.142	0.000	0.000	0.000	0.000
50	D	52	VAL	0	-0.022	-0.008	13.804	0.021	0.021	0.000	0.000	0.000	0.000
51	D	53	ARG	1	0.894	0.940	14.943	0.119	0.119	0.000	0.000	0.000	0.000
52	D	54	ASN	0	-0.037	-0.011	17.117	0.002	0.002	0.000	0.000	0.000	0.000
53	D	55	ARG	1	0.949	0.970	17.414	0.248	0.248	0.000	0.000	0.000	0.000
54	D	56	VAL	0	0.027	0.015	17.817	0.021	0.021	0.000	0.000	0.000	0.000
55	D	57	ASN	0	-0.073	-0.038	19.771	-0.041	-0.041	0.000	0.000	0.000	0.000
56	D	58	PHE	0	0.046	0.022	17.029	0.018	0.018	0.000	0.000	0.000	0.000
57	D	59	ARG	1	0.960	0.985	21.962	0.213	0.213	0.000	0.000	0.000	0.000
58	D	60	GLY	0	0.077	0.038	24.280	0.012	0.012	0.000	0.000	0.000	0.000
59	D	61	SER	0	-0.031	0.012	25.020	-0.010	-0.010	0.000	0.000	0.000	0.000
60	D	62	LEU	0	-0.002	-0.012	18.885	-0.007	-0.007	0.000	0.000	0.000	0.000
61	D	63	ASN	0	-0.062	-0.023	22.131	0.009	0.009	0.000	0.000	0.000	0.000
62	D	64	THR	0	0.001	-0.015	19.766	-0.002	-0.002	0.000	0.000	0.000	0.000
63	D	65	TYR	0	0.021	-0.003	16.781	-0.024	-0.024	0.000	0.000	0.000	0.000
64	D	66	ARG	1	0.952	0.975	14.103	0.473	0.473	0.000	0.000	0.000	0.000
65	D	67	PHE	0	0.006	0.015	9.143	-0.037	-0.037	0.000	0.000	0.000	0.000
66	D	68	CYS	0	0.003	-0.007	11.007	0.159	0.159	0.000	0.000	0.000	0.000
67	D	69	ASP	-1	-0.883	-0.926	8.113	-0.719	-0.719	0.000	0.000	0.000	0.000
68	D	70	ASN	0	-0.052	-0.038	6.227	-0.355	-0.355	0.000	0.000	0.000	0.000
69	D	71	VAL	0	0.002	0.006	5.325	-0.760	-0.760	0.000	0.000	0.000	0.000
70	D	72	TRP	0	0.015	0.008	7.555	0.491	0.491	0.000	0.000	0.000	0.000
71	D	73	THR	0	-0.064	-0.035	10.252	0.070	0.070	0.000	0.000	0.000	0.000
72	D	74	PHE	0	-0.012	-0.012	12.663	0.056	0.056	0.000	0.000	0.000	0.000
73	D	75	VAL	0	-0.026	-0.018	15.867	0.023	0.023	0.000	0.000	0.000	0.000
74	D	76	LEU	0	-0.018	-0.002	18.293	0.005	0.005	0.000	0.000	0.000	0.000
75	D	77	ASN	0	0.023	0.001	21.263	0.006	0.006	0.000	0.000	0.000	0.000
76	D	78	ASP	-1	-0.891	-0.945	24.638	-0.178	-0.178	0.000	0.000	0.000	0.000
77	D	79	VAL	0	-0.079	-0.037	21.025	-0.009	-0.009	0.000	0.000	0.000	0.000
78	D	80	GLU	-1	-0.901	-0.977	24.301	-0.153	-0.153	0.000	0.000	0.000	0.000
79	D	81	PHE	0	-0.043	-0.030	17.657	-0.017	-0.017	0.000	0.000	0.000	0.000
80	D	82	ARG	1	0.904	0.946	22.628	0.187	0.187	0.000	0.000	0.000	0.000
81	D	83	GLU	-1	-0.823	-0.911	20.758	-0.222	-0.222	0.000	0.000	0.000	0.000
82	D	84	VAL	0	0.009	-0.016	23.722	0.013	0.013	0.000	0.000	0.000	0.000
83	D	85	THR	0	-0.048	0.005	26.305	0.007	0.007	0.000	0.000	0.000	0.000
84	D	86	GLU	-1	-0.887	-0.951	28.165	-0.140	-0.140	0.000	0.000	0.000	0.000
85	D	87	LEU	0	-0.045	-0.049	26.304	-0.011	-0.011	0.000	0.000	0.000	0.000
86	D	88	ILE	0	0.047	0.052	21.756	0.007	0.007	0.000	0.000	0.000	0.000
87	D	89	LYS	1	0.869	0.947	24.860	0.129	0.129	0.000	0.000	0.000	0.000
88	D	90	VAL	0	-0.007	0.004	21.564	0.007	0.007	0.000	0.000	0.000	0.000
89	D	91	ASP	-1	-0.796	-0.886	24.882	-0.152	-0.152	0.000	0.000	0.000	0.000
90	D	92	LYS	1	0.918	0.943	21.158	0.172	0.172	0.000	0.000	0.000	0.000
91	D	93	VAL	0	0.002	0.018	16.881	0.008	0.008	0.000	0.000	0.000	0.000
92	D	94	LYS	1	0.941	0.974	13.904	0.319	0.319	0.000	0.000	0.000	0.000
93	D	95	ILE	0	0.005	0.004	12.042	0.008	0.008	0.000	0.000	0.000	0.000
94	D	96	VAL	0	0.006	0.007	7.602	-0.022	-0.022	0.000	0.000	0.000	0.000
95	D	97	ALA	0	-0.012	-0.012	7.637	0.096	0.096	0.000	0.000	0.000	0.000
96	D	98	CYS	0	-0.005	0.005	2.547	-1.728	-0.548	2.196	-0.896	-2.479	0.005
97	D	99	ASP	-1	-0.929	-0.953	2.609	-8.272	-6.215	0.766	-0.987	-1.836	-0.009

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Interactive mode: IFIE and PIEDA for fragment #1(D:3:TYR)